Santos said he will receive local anesthesia and not delegate his powers as head of state.
"I am at ease because this cancer was detected quite early, as I underwent tests every year," he told a news conference.
He said doctors have advised him not travel for a few weeks after the operation but that otherwise his overall health is not in jeopardy.
Santos said he will travel to Lima later on Monday to attend a summit of Latin American and Arab leaders and return on Tuesday.